Conformational preferences of non-prolyl and prolyl residues

The conformational study on Ac-Ala-NHMe (the alanine dipeptide) and Ac-Pro-NHMe (the proline dipeptide) is carried out using ab initio HF and density functional methods with the self-consistent reaction field method to explore the differences in the backbone conformational preference and the cis-trans isomerization for the non-prolyl and prolyl residues in the gas phase and in the solutions (chloroform and water). For the alanine and proline dipeptides, with the increase of solvent polarity, the populations of the conformation tC with an intramolecular C(7) hydrogen bond significantly decrease, and those of the polyproline II-like conformation tF and the alpha-helical conformation tA increase, which is in good agreement with the results from circular dichroism and NMR experiments. For both the dipeptides, as the solvent polarity increases, the relative free energy of the cis conformer to the trans conformer decreases and the rotational barrier to the cis-trans isomerization increases. It is found that the cis-trans isomerization proceeds in common through only the clockwise rotation with omega' approximately +120 degrees about the non-prolyl and prolyl peptide bonds in both the gas phase and the solutions. The pertinent distance d(N...H-N(NHMe)) can successfully describe the increase in the rotational barriers for the non-prolyl and prolyl trans-cis isomerization as the solvent polarity increases and the higher barriers for the non-prolyl residue than for the prolyl residue, as seen in experimental and calculated results. By analysis of the contributions to rotational barriers, the cis-trans isomerization for the non-prolyl and prolyl peptide bonds is proven to be entirely enthalpy driven in the gas phase and in the solutions. The calculated cis populations and rotational barriers to the cis-trans isomerization for both the dipeptides in chloroform and/or water accord with the experimental values.     

甲基丙烯酸甲酯聚合动力学和分子量模型及仿真

考虑甲基丙烯酸甲酯聚合过程中体积收缩，反应物和生成物的浓度变化，以及由于凝胶、玻璃化和笼闭等效应对各速率常数和物性参数的影响，从基元反应和物料平衡出发，推导了半间歇，有链转移剂参与情况下的聚合动力学和分子量模型。用模型仿真计算了聚合温度、引发剂、溶剂和链转移剂的种类和浓度等对甲基丙烯酸甲酯聚合动力学和聚合过程中分子量变化的影响规律，并与实验和文献数据进行比较。     

Measurement of protein-DNA interaction parameters by electrophoresis mobility shift assay

Native gel electrophoresis (mobility shift) assays may be used to obtain quantitative information about the site distribution, equilibria and kinetics of protein-DNA interactions. These applications depend on the ability of the electrophoretic system to resolve the reaction components, and on their stabilities during the separation process. Factors which affect the lifetimes and mobilities of protein-DNA complexes during electrophoresis include reaction and electrophoresis buffer composition, pH, and ionic strength; the presence of low molecular weight effectors and enzymatic substrates; the nature and concentration of the gel matrix; the temperature; the molecular weights of protein and DNA; the stoichiometric ratios of their complexes; and the possibility of conformational and configurational isomerization of reaction components. We discuss how these factors influence the acquisition of quantitative data from electrophoretic patterns and band intensities, and present formulas for the estimation of equilibrium constants and rate constants for prototypical DNA-protein interactions.     

扬帆启航：电化学实验初步

电化学是研究电能和化学能相互转化的规律的科学。电能和化学能之间的相互转换,是通过电极/电解质溶液表界面的结构变化和电荷转移反应来实现的。以电化学能源器件为例,前者为超级电容器,能量存储和释放主要通过界面双电层的表界面结构变化来实现;后者为化学电源,能量存储和释放主要通过电极活性物质的表界面化学反应来实现。所以,研究一个电化学体系时,主要关注两个问题,即表界面结构和表界面电荷转移反应。而表界面结构直接影响表界面电荷转移反应的性质,因此,从电化学实验的角度,表界面的构筑是至关重要的,包括电极的制备和表征、电极修饰材料的制备及组装、溶剂和支持电解质的选择和优化、电化学实验环境等等。本文旨在向广大电化学初学者讲述电化学实验的准备工作以及对实验现场数据的基本判断,帮助大家在实验中及时发现问题,及早采取措施,高效率地获取可信的实验数据。     

Phenolic potential of Tannat, Cabernet-Sauvignon and Merlot grapes and their correspondence with wine composition

The phenolic potential of Tannat, Cabernet-Sauvignon and Merlot grapes was evaluated in 2001 and 2002 and its correspondence with the colour and composition of the respective wines was established. Three vineyards of each variety, situated in the south of Uruguay were considered. Two samples of each vineyard were taken at the moment of the harvest. Phenolic richness, extractable anthocyanins contents and total potential in anthocyanins of the grapes were estimated. Two fermentations on skins were carried out for each vineyard using 50 kg of grape in each one. The anthocyanic and total polyphenols contents of the musts were analysed every 24 h, and skins extractions were carried out in parallel in the laboratory. The duration of the maceration for each variety was decided in function of the analytical results in the grapes, musts and skins extractions. Wines were analysed 2 months after the alcoholic fermentation, determining its phenolic composition and colour. Tannat grapes presented anthocyanic and total polyphenols contents significantly higher in both years. Therefore, wines from this variety presented colour intensity and phenolic contents statistically higher than Cabernet-Sauvignon and Merlot. The correlations between the phenolic contents of the grapes, skins, musts and wines were very significant. Colour intensity and phenolic contents of the wines were highly correlated with the total polyphenols of the grapes and with anthocyanins of the grapes, skins, musts and wines. The estimate of the phenolic potential of the grapes and the extractability of the pigments allows to manage more adequately the fermentation on skins and is an interesting tool to predict the colour and the composition of the wines.     

Contributions to the Chemistry of the Binary Compounds of the Transition Elements

Phase and structural relationships of the sulfur, selenium, and tellurium compounds of the 4d and 5d transition elements of groups IV to VII of the periodic system are discussed. Homologous elements behave very similarly with respect to the chalcogens, and this is particularly the case for niobium and tantalum, and for molybdenum and tungsten. However, zirconium, niobium, and molybdenum have a greater tendency towards formation of chalcogen-poor phases than their homologues hafnium, tantalum, and tungsten. Subchalcogenides are known only for zirconium and niobium. The number of phases and the tendency towards formation of solid solutions are considerably smaller among the tellurides than among the sulfides and selenides. The crystal structures of the telluride phases also differ from those of the sulfide and selenide phases of analogous composition. In addition, a review of the phase and structural relationships of the arsenic and antimony compounds of the 4d and 5d transition elements of groups V to VII is given.     

视网膜脱离后PVR的形成与氧自由基和锌、铜关系的研究

为探讨氧自由基和锌、铜在视网膜脱离后增殖性玻璃体视网膜病变 (PVR)中的作用 ,收集了 48例视网膜脱离患者视网膜下液 (SRF) ,利用紫外分光光度计测定了SRF中LPO的含量和SOD的活性 ,用原子吸收光谱法测定了Zn、Cu的含量。结果表明 ,随着PVR程度及玻璃体浑浊的加重、病程的延长 ,LPO含量增加 ,SOD活性明显下降 ,P <0 0 5 ,差异有统计学意义。提示SRF中LPO、Zn、Cu含量及SOD活性的改变与视网膜脱离后PVR的发生、发展有密切关系。     

Excited state properties of the chromophore of the asFP595 chromoprotein: 2D and 3D theoretical analyses

The ground and excited state properties (e.g., the intramolecular charge and energy transfer, and electron‐hole coherence) of the chromophore of the asFP595 chromoprotein from Anemonia sulcata in the neutral and anionic forms are theoretically studied with quantum chemistry methods. The ground‐state properties of the asFP595 in the neutral and anionic forms, such as the alternations of the bond lengths and the Mulliken charge distributions, are compared. The calculated transition energies of the asFP595 in the neutral and anionic form are consistent with the experimental results. To study the excited state properties of the asFP595 chromophore, the energies and densities of highest occupied molecular orbitals (HOMOs) and lowest unoccupied molecular orbitals (LUMOs), as well as the CI main coefficients, are compared between the two forms. The intramolecular charge and energy transfer in the neutral and anionic forms are investigated and compared with the three‐dimensional (3D) real‐space analysis methods, including the strength and orientation of the transition dipoles with transition density, and the orientation and result of the intramolecular charge transfer with charge difference density. The electron‐hole coherence and delocalization on the excitation are studied with the 2D real‐space analysis method of the transition density matrix. In all, the calculated results are remain in good agreement with the experimental data, and the theoretical analysis results supported the proposed models in the experiment. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Effect of the Head Group of Surfactant on the Miscibility of Sodium Chloride and Surfactant in an Adsorbed Film and Micelle

The thermodynamic treatment of a surfactant mixture was applied to the mixture of sodium chloride, NaCl, with octyl methyl sulfoxide (OMS) and that with decyldimethylphosphine oxide (DePO). The surface tension of aqueous solutions of the mixtures was measured as a function of the total concentration and the composition of the mixtures at 298.15 K. The total surface densities of the mixtures and the composition of the adsorbed films and micelles were evaluated by applying thermodynamic equations to the expeimental results. It was found that the adsorbed film and micelle are almost composed of the surfactant and there is slight attractive interaction between the ions of NaCl and the head groups of OMS and DePO molecules in the adsorbed films and micelles. A difference in the miscibility of NaCl and surfactant was observed between the OMS and DePO systems and attributed to the difference in the hydration of the head group between OMS and DePO molecules. The comparison of these results with those of the mixtures of NaCl with tetraethylene glycol monooctyl ether (C(8)E(4)) and dodecylammonium chloride (DAC) indicated that the small difference in the miscibility in an adsorbed film and micelle among these nonionic surfactant systems arises from the difference in hydration and structure of the head groups and the large one between the nonionic surfactant and DAC systems results from electrostatic interactions between dodecylammonium and sodium ions. Copyright 2001 Academic Press.     

Fabrication of open‐porous PCL/PLA tissue engineering scaffolds and the relationship of foaming process,morphology, and mechanical behavior

Tissue engineering scaffolds should provide a suitable porous structure and proper mechanical strength, which is beneficial for the delivery of growth factor and regulation of cells. In this study, the open‐porous polycaprolactone (PCL)/poly (lactic acid) (PLA) tissue engineering scaffolds with suitable porous scale were fabricated using different ratios of PCL/PLA blends. At the same time, the relationship of foaming process, morphology, and mechanical behavior in the optimized batch microcellular foaming process were studied based on the single‐factor experiment method. The porous structures and mechanical strength of the scaffolds were optimized by adjusting foaming parameters, including the temperature, pressure, and CO₂ dissolution time. The results indicated that the foaming parameters influence the cell morphology, further determine the mechanical behavior of PCL/PLA blends. When the PCL content is high, with the increase of temperature and time, the cell diameter and the elastic modulus increased, and the tensile strength and elastic modulus increased with the increase of the average cell size, and decreased as the increase of the cell density. While when the PLA content was high, the cell diameter showed the same trend, and the tensile strength and elastic modulus were higher, and the elongation at break was lower, and tensile strength and elastic modulus decreased with the increase of the average cell size and increased with the increase of cell density. This work successfully fabricated optimized porous PCL/PLA scaffolds with excellent suitable mechanical properties, pore sizes, and high interconnectivity, indicating the effectiveness of modulating the batch foaming process parameters.     

单体结构对基于离子作用的自修复光固化材料性能的影响

本文研究了单体结构及其比例对基于离子作用的自修复光固化材料光聚合行为、力学性能,以及自修复性能的影响。结果表明：改变软硬单体种类及其比例不会改变自修复光固化体系的光聚合行为。增加软单体含量和降低硬单体含量,材料的拉伸应变和修复效率随之增加,断裂应力随之降低。硬单体中刚性环会增加聚合物链间的内摩擦力,使材料断裂应力增加,软单体中柔性醚链则降低链间范德华力,增强链移动性,提高材料的拉伸应变和修复效率。软单体为丙烯酸正丁酯（BA）及硬单体为丙烯酸异冰片酯（IBOA）的样品IB7-BA3展现出较好的综合性能,断裂应力为1.42 MPa,拉伸应变为295%,修复效率高于90%。     

A Hirshfeld-I interpretation of the charge distribution, dipole and quadrupole moments of the halogenated acetylenes FCCH, ClCCH, BrCCH, and ICCH

We report the dipole and quadrupole moments of the halogenated acetylenes calculated using large basis sets and the SCF, DFT(B3LYP), and CCSD methods, and we analyze the charge density using the Hirshfeld and Hirshfeld-I techniques. The atomic charges, dipoles, and quadrupoles resulting from the Hirshfeld-I analysis are used to interpret the unusually small molecular dipole moments in the sequence as well as the molecular quadrupole moments. The very small dipoles obtain for two reasons. First, the dipole moment associated with the σ and π electron densities is comparable in magnitude and opposite in direction. Second, the charge and induced dipole contributions for ClCCH, BrCCH, and ICCH have opposite signs further reducing the molecular dipoles. The molecular quadrupole moments are the sum of a charge, atomic dipole, and in situ quadrupole terms, and are dominated by the atomic dipoles and in situ quadrupoles with the charge contributions playing an unexpectedly minor role.     

Enhancement of coherent energy transport by disorder and temperature in light harvesting processes

We investigate the influence of static disorder and thermal excitations on excitonic energy transport in the light-harvesting apparatus of photosynthetic systems by solving the Schro?dinger equation and taking into account the coherent hoppings of excitons, the rates of exciton creation and annihilation in antennas and reaction centers, and the coupling to thermally excited phonons. The antennas and reaction centers are modeled, respectively, as the sources and drains which provide the channels for creation and annihilation of excitons. Phonon modes below a maximum frequency are coupled to the excitons that are continuously created in the antennas and depleted in the reaction centers, and the phonon population in these modes obeys the Bose-Einstein distribution at a given temperature. It is found that the energy transport is not only robust against the static disorder and the thermal noise, but it can also be enhanced by increasing the randomness and temperature in most parameter regimes. Relevance of our work to the highly efficient energy transport in photosynthetic systems is discussed.     

脑部磁共振结合静息态fMRI方法在卒中患者认知障碍中的应用

本研究主要探讨脑部磁共振结合静息态fMRI方法在卒中患者认知障碍中的应用。本研究将符合卒中认知障碍患者25例设为患者组,将25例健康者设为对照组。采用脑部静息态核磁共振对实验者进行扫描,以脑部双侧海马为种子点进行功能连接分析,并通过软件分析两组实验者静息态双侧海马差异。结果发现,与对照组相比,患者组右侧海马与左右侧额中回、左侧额下回等的连接减少;右侧海马与左侧颞上中回、双侧丘脑的连接增加;左侧海马与左侧颞额中回、右侧颞额上回、右侧额下回的连接减少;左侧海马与右侧顶下回连接增加。总之,本研究发现卒中患者海马脑区与颞叶皮层、额叶皮层之间的连接减少,可能是由卒中患者脑损害导致。     

在专业建设中培养大学生的科技创新能力

结合哈尔滨工业大学材料化学专业建设情况,重点阐述了专业建设与大学生科技创新能力培养的关系以及所获得的成果。在科技创新中完善专业建设,在专业建设中为科技创新活动搭建舞台,着重培养本科生的科学精神和科研能力。利用专业建设和科技创新的协同育人机制,实现专业与育人的有机结合,提高学生的综合素质和创新能力。     

Numerical simulation of bubble dynamics in a micro-channel under a nonuniform electric field

A numerical method is used to simulate the motion and coalescence of air bubbles in a micro-channel under a nonuniform electric field. The channel is equipped with arrays of electrodes embedded in its wall and voltages are applied on the electrodes to generate a specified electric field gradient in the longitudinal direction. In the study, the Navier-Stokes equations are solved by using the level set method handling the deformable/moving interfaces between the bubbles and the ambient liquid. Both the polarization Coulomb force and the dielectrophoresis force are considered as the force source of the Navier-Stokes equations by solving the Maxwell's equations. The flow field equations and the electric field equations are coupled and solved by using the finite element method. The electric field characteristics and the dynamic behavior of a bubble are analyzed by studying the distributions of the electric field and the force, the deformation and the moving velocity of the air bubble. The result suggests that the model of dispersed drops suspended in the immiscible dielectric liquid and driven by a nonuniform electric field is an effective method for the transportation and coalescence of micro-drops.     

Temperature Dependence of Transport Properties of Liquid Sodium and Potassium

The electrical and thermal resistivities of liquid Na and K are calculated over a range of temperature at and above the melting point using the solutions of the Boltzmann equation, the form factors constructed using the Dagens-Rasolt-Taylor (DRT) model potential, the screening function of Geldart and Taylor and the X-ray structure factors of Waseda. The ratio of the electrical and the thermal resistivities is compared with the Wiedemann-Franz law and with experiment. We show that the deviation from the Lorenz number can be explained by the inelastic part of the electron-phonon scattering and the electron-electron scattering.     

A biophysical perspective of understanding nanoparticles at large

In this article we present a biophysical perspective that describes the fate of nanoparticles in both the aqueous phase and in living systems. Specifically, we show the correlations between the physicochemistry of fullerenes and their uptake, translocation, transformation, transport, and biodistribution in mammalian and plant systems, at the molecular, cellular, and whole organism level. In addition to fullerenes and their structural derivatives, we describe the biological and environmental implications and applications of the condensed matter of carbon nanotubes and quantum dots, and the soft condensed matter of plastic and dendrimers. The main purpose of this article is to demonstrate the vast opportunities and unique advantages of applying experimental and simulation biophysics to the nascent research field of understanding nanoparticles at large.